Haplotype combination of SREBP-1c gene sequence variants is associated with growth traits in cattle

Genome ◽  
2011 ◽  
Vol 54 (6) ◽  
pp. 507-516 ◽  
Author(s):  
Yong-Zhen Huang ◽  
Hua He ◽  
Jia-Jie Sun ◽  
Jing Wang ◽  
Zhuan-Jian Li ◽  
...  
Keyword(s):  
Growth Traits ◽  
Regulatory Element ◽  
Large Deletion ◽  
Silent Mutation ◽  
Sequence Variants ◽  
Missense Mutations ◽  
Cattle Breeds ◽  
Pcr Rflp ◽  
Element Binding Protein ◽  
Strong Candidate

The aim of this study was to examine the association of the SREBP-1c polymorphism with growth traits in cattle breeds. Five sequence variants (SVs) were identified within the bovine sterol regulatory element-binding protein-1c gene (SREBP-1c), using DNA sequencing, PCR, PCR–RFLP, and forced PCR–RFLP methods. These polymorphisms include three missense mutations (SV1, SV4, and SV5) in exons 7, 9, and 12, a silent mutation (SV3) in exon 9, and a large deletion (SV2) in intron 7. Overall, we report the validation of polymorphisms within the bovine SREBP-1c gene, and the haplotype variability and extent of linkage disequilibrium (LD) in 1061 individuals representing the five main cattle breeds from China. We also investigated haplotype frequencies and LD coefficients for five SVs in all study populations. LD and haplotype structure of SREBP-1c were different between breeds. The result of haplotype analysis of five SVs showed that 27 different haplotypes were identified by all breeds. Two haplotypes (Hap1 and Hap2) shared by all five populations accounted for 42.75%, 35.68%, 36.44%, 25.43%, and 96.26% of all haplotypes observed in the cattle breeds Nanyang, Qinchuan, Jiaxian, Jinnan, and Chinese Holstein, respectively. The statistical analyses indicated that one single SV and 38 combined haplotypes were significantly associated with growth traits in the Nanyang cattle population (P < 0.05 or P < 0.01). The results of this study suggest that the SREBP-1c gene possibly is a strong candidate gene that affects growth traits in the Chinese beef cattle breeding program.

Haplotype combination of the bovine INSIG1 gene sequence variants and association with growth traits in Nanyang cattle

Genome ◽  
2012 ◽  
Vol 55 (6) ◽  
pp. 429-436 ◽  
Author(s):  
Jiajie Sun ◽  
Yuan Gao ◽  
Dong Liu ◽  
Wei Ma ◽  
Jing Xue ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Growth Traits ◽  
Regulatory Element ◽  
Sequence Variants ◽  
Coding Region ◽  
Dna Pooling ◽  
Proteolytic Activation ◽  
Haplotype Combination ◽  
Pcr Rflp ◽  
Sterol Regulatory Element

The insulin-induced gene 1 (INSIG1) gene encodes a protein that blocks proteolytic activation of sterol regulatory element binding proteins, which are transcription factors that activate genes that regulate cholesterol, fatty acid, and glucose metabolism. However, similar research for the bovine INSIG1 gene is lacking. Therefore, in this study, polymorphisms of the bovine INSIG1 gene were detected in 643 individuals from four cattle breeds by DNA pooling, forced PCR–RFLP, PCR–SSCP, and DNA sequencing methods. Only 10 novel SNPs were identified, which included four mutations in the coding region and the others in the introns. In Nanyang individuals, seven common haplotypes were identified based on four coding region SNPs. The haplotype GACT, with a frequency of 75.4%, was the most prevalent haplotypes and SNPs formed two linkage disequilibrium blocks with strong multi-allelic D′ (D′ = 1). Additionally, association analysis between mutations of the bovine INSIG1 gene and growth traits in Nanyang cattle at 6, 12, 18, and 24 months old was performed, and the results indicated that the polymorphisms were not significantly associated with body mass.

Polymorphisms of the Myostatin gene (MSTN) and its associationwith growth traits in Bali cattle

2017 ◽  
Author(s):  
Hary Nugroho ◽  
Woro Busono ◽  
Sucik Maylinda
Keyword(s):  
Growth Traits ◽  
Restriction Enzymes ◽  
Gene Frequencies ◽  
Gene Markers ◽  
Myostatin Gene ◽  
Pcr Rflp ◽  
Chest Girth ◽  
Bali Cattle ◽  
Strong Candidate ◽  
Almost All

This research aims to develop a method for selection based on myostatin gene markers. The experiment was conducted in Bali cattle. Blood samples were collected from 100 cattle irrespective of age. PCR-RFLP was applied with primers for amplifying the 1346bp of the Myostatin gene were (F) 5’-CCCTACAGAGGCCACTTCAA-3’ and (R) 5’-CTCGCTGTTCTCATTCAGATC-3’, sand HaeIII restriction enzymes. PCR-RFLP results showed that not all genotypes present in the population, despite populations that were observed quite polymorphic (PIC = 49.5%) with the conditions of gene frequencies. The results showed that almost all variables influenced by myostatin genotype where the genotype BB is better, except the chest girth showed a better result in genotype AB. It suggested that MSTN is strong candidate gene that influenced growth traits. Moreover, it is also expected that this MSTN could be used in marker-assisted selection.

Exploring polymorphisms and associations of the bovine MOGAT3 gene with growth traits

Genome ◽  
2012 ◽  
Vol 55 (1) ◽  
pp. 56-62 ◽  
Author(s):  
Jiajie Sun ◽  
Chunlei Zhang ◽  
Xianyong Lan ◽  
Chuzhao Lei ◽  
Hong Chen
Keyword(s):  
Growth Traits ◽  
Enzymatic Reaction ◽  
Fatty Acyl ◽  
Missense Mutations ◽  
Coding Region ◽  
Dna Pooling ◽  
Qinchuan Cattle ◽  
Rate Limiting Step ◽  
Pcr Rflp ◽  
Acyl Coenzyme A

Monoacylglycerol acyltransferase (MGAT3, also known as MOGAT3) catalyzes the synthesis of diacylglycerol (DAG) using 2-monoacylglycerol and fatty acyl coenzyme A. This enzymatic reaction is believed to be an essential and rate-limiting step for the absorption of dietary fat in the small intestine. However, similar research for the bovine MOGAT3 gene is lacking. Therefore, in this paper, polymorphisms of the bovine MOGAT3 gene were detected in 1145 individuals from five cattle breeds by DNA pooling, PCR–RFLP, and DNA sequencing methods. The results showed that 26 novel SNPs were identified, which included 16 mutations in the coding region and the others in the introns. Additionally, association analysis between two missense mutations, g.A229G and g.G1627A, and growth traits in Nanyang cattle up to 2 years of age and adult Qinchuan cattle was performed. The results indicated that polymorphisms were significantly associated with Nanyang cattle, but no convincing associations were observed for Qinchuan cattle for the studied traits.

Exploring polymorphisms and potential application roles of the bovine Nfix gene in breeding

Genome ◽  
2012 ◽  
Vol 55 (12) ◽  
pp. 845-851 ◽  
Author(s):  
Yang Zhou ◽  
Xianyong Lan ◽  
Yao Xu ◽  
Bao Zhang ◽  
Mijie Li ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Haplotype Analysis ◽  
Growth Traits ◽  
Multiple Forms ◽  
Single Nucleotide ◽  
Multiple Alleles ◽  
Cattle Breeds ◽  
Pcr Rflp ◽  
Multiple Alternative ◽  
Nuclear Factor I

The aim of this study was to detect mutations of the nuclear factor I/X (Nfix) gene and examine the association of its polymorphisms with growth traits in cattle. Six sequence variants (SVs) including five single-nucleotide mutations and an indel with multiple alleles were detected, among which four polymorphisms within the Nfix gene were identified in 1159 individuals of five cattle breeds by sequencing and forced PCR–RFLP methods. The results of haplotype analysis showed 14 haplotypes within the breeds. Three haplotypes were shared by the five cattle breeds. Hap1 (ACAI) was extremely predominant in all test populations, which suggested that individuals with Hap1 (ACAI) were more adapted to the steppe environment. Association analysis in Nanyang cattle showed that two SVs of the Nfix gene were significantly associated with growth traits at different ages. In addition, the locations of the SVs showed that the 3′ terminal of the bovine Nfix gene was unstable. Combining this instability with its characteristic of multiple alternative splicing, we conjectured that some SVs might have a relationship with the formation of the splices through which growth traits are modulated. This study will provide useful information for the selection and detection of multiple forms of alternative splicing of the bovine Nfix gene.

Comparative analysis of the IGF2 and ZBED6 gene variants and haplotypes reveals significant effect of growth traits in cattle

Genome ◽  
2013 ◽  
Vol 56 (6) ◽  
pp. 327-334 ◽  
Author(s):  
Yong-Zhen Huang ◽  
Zhao-Yang Zhan ◽  
Yu-Jia Sun ◽  
Jing Wang ◽  
Ming-Xun Li ◽  
...  
Keyword(s):  
Body Mass ◽  
Growth Traits ◽  
Muscle Growth ◽  
Missense Mutations ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Mutant Type ◽  
Cattle Breeds ◽  
Proliferation And Differentiation ◽  
Different Ages

Muscle growth is a complex phenomenon regulated by many factors, whereby net growth results from the combined action of synthesis and turnover. Insulin-like growth factor 2 (IGF2) is a fetal growth and differentiation factor that plays an important role in muscle growth and in myoblast proliferation and differentiation; Zinc finger, BED-type containing 6 (ZBED6) is a novel transcription factor that was identified and shown to act as a repressor of IGF2 transcription in skeletal muscle. In this study, a total of seven single nucleotide polymorphisms (SNPs) were identified, four SNPs in intron 8 of IGF2 and one promoter SNP and two missense mutations in the coding region of ZBED6, two of which were in complete linkage disequilibrium (LD) in the bovine IGF2. The 58 haplotypes were inferred in 1522 individuals representing four purebred cattle breeds from China. The seven SNPs, 79 and 66 combined diplotypes were revealed for association with body mass in Nanyang and Jiaxian cattle populations at five different ages (P < 0.05 or 0.01). The mutant-type variants and haplotype 58 (likely in LD with the beneficial quantitative trait nucleotide allele) was superior for body mass; the heterozygote diplotype of the most common haplotypes 58 was associated with higher body mass compared to either heterozygote or homozygote. The statistical analyses indicated that the mutant-type variants and haplotypes are significantly associated with body mass in study cattle populations at different ages. These data demonstrate that variants and haplotypes are associated with growth traits, and these results may provide important biological insights into the phenotypic differentiation that is associated with adaptation and specialization of cattle breeds.

scholarly journals The Association of an SNP in the EXOC4 Gene and Reproductive Traits Suggests Its Use as a Breeding Marker in Pigs

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 521
Author(s):  
Yingting He ◽  
Xiaofeng Zhou ◽  
Rongrong Zheng ◽  
Yao Jiang ◽  
Zhixiang Yao ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Fragment Length Polymorphism ◽  
Regulatory Element ◽  
Reproductive Traits ◽  
Specific Sequence ◽  
Litter Weight ◽  
Potential Binding ◽  
Pcr Rflp ◽  
Teat Number ◽  
Myeloid Zinc Finger

In mammals, the exocyst complex component 4 (EXOC4) gene has often been reported to be involved in vesicle transport. The SNP rs81471943 (C/T) is located in the intron of porcine EXOC4, while six quantitative trait loci (QTL) within 5–10 Mb around EXOC4 are associated with ovary weight, teat number, total offspring born alive, and corpus luteum number. However, the molecular mechanisms between EXOC4 and the reproductive performance of pigs remains to be elucidated. In this study, rs81471943 was genotyped from a total of 994 Duroc sows, and the genotype and allele frequency of SNP rs81471943 (C/T) were statistically analyzed. Then, the associations between SNP rs81471943 and four reproductive traits, including number of piglets born alive (NBA), litter weight at birth (LWB), number of piglets weaned (NW), and litter weight at weaning (LWW), were determined. Sanger sequencing and PCR restriction fragment length polymorphism (PCR-RFLP) were utilized to identify the rs81471943 genotype. We found that the genotype frequency of CC was significantly higher than that of CT and TT, and CC was the most frequent genotype for NBA, LWB, NW, and LWW. Moreover, 5′-deletion and luciferase assays identified a positive transcription regulatory element in the EXOC4 promoter. After exploring the EXOC4 promoter, SNP −1781G/A linked with SNP rs81471943 (C/T) were identified by analysis of the transcription activity of the haplotypes, and SNP −1781 G/A may influence the potential binding of P53, E26 transformation specific sequence -like 1 transcription factor (ELK1), and myeloid zinc finger 1 (MZF1). These findings provide useful information for identifying a molecular marker of EXOC4-assisted selection in pig breeding.

Sign in / Sign up

Export Citation Format

Share Document